[phenixbb] cis peptide

[Ralf W. Grosse-Kunstleve]

Hi Jianghai,

> Does phenix.refine restrain cis peptide?

Yes, controlled via this parameter scope:

    peptide_link {
      cis_threshold = 45
      discard_psi_phi = True
      omega_esd_override_value = None
    }

> How do I know if the refined
> pdb file contain any cis peptide?

In theory you could tell by inspecting the .geo file, but it is difficult
to pin-point the cis peptide restraints. Probably, it is better to use
e.g. the pdb deposition tools or something similar to get a listing of
the cis peptides.

I'll add "list cis peptides" to our to-do list.

Ralf